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Iodine in PDB 6dog: Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C

Enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C

All present enzymatic activity of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C:
3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C, PDB code: 6dog was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.27 / 1.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.574, 37.889, 62.247, 90.00, 96.22, 90.00
R / Rfree (%) 16.1 / 18.3

Other elements in 6dog:

The structure of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C (pdb code 6dog). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C, PDB code: 6dog:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 6dog

Go back to Iodine Binding Sites List in 6dog
Iodine binding site 1 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:14.8
occ:0.45
HH A:TYR83 2.5 22.2 1.0
HD22 A:LEU161 3.2 27.2 1.0
HD13 A:LEU161 3.3 28.8 1.0
OH A:TYR83 3.3 18.5 1.0
HD13 A:LEU111 3.4 15.9 1.0
HE2 A:TYR83 3.4 18.9 1.0
HB3 A:LEU161 3.4 18.8 1.0
HD22 A:LEU111 3.4 16.4 1.0
HD3 A:ARG97 3.5 23.1 1.0
HB3 A:LEU111 3.5 13.8 1.0
O A:HOH379 3.5 20.7 1.0
O A:HOH362 3.7 16.5 1.0
HH11 A:ARG97 3.7 33.9 1.0
CD2 A:LEU161 4.1 22.7 1.0
CE2 A:TYR83 4.1 15.7 1.0
CZ A:TYR83 4.2 16.0 1.0
CD1 A:LEU161 4.2 24.0 1.0
NH1 A:ARG97 4.3 28.2 1.0
CD1 A:LEU111 4.3 13.3 1.0
CB A:LEU161 4.3 15.7 1.0
O A:HOH307 4.3 35.9 1.0
C3 A:GOL212 4.3 42.2 1.0
CD2 A:LEU111 4.3 13.7 1.0
CB A:LEU111 4.4 11.5 1.0
CG A:LEU161 4.4 17.6 1.0
HG2 A:ARG97 4.4 20.4 1.0
CD A:ARG97 4.4 19.2 1.0
O3 A:GOL212 4.5 25.9 1.0
HD21 A:LEU161 4.6 27.2 1.0
CG A:LEU111 4.6 12.8 1.0
HH12 A:ARG97 4.6 33.9 1.0
HD23 A:LEU161 4.6 27.2 1.0
HD11 A:LEU161 4.6 28.8 1.0
HD11 A:ILE100 4.7 23.1 1.0
HB2 A:HIS115 4.7 14.2 1.0
HD11 A:LEU111 4.8 15.9 1.0
HB2 A:LEU161 4.8 18.8 1.0
HD21 A:LEU111 4.8 16.4 1.0
HD12 A:LEU161 4.8 28.8 1.0
HD12 A:LEU111 4.9 15.9 1.0
HB2 A:LEU111 4.9 13.8 1.0
HD23 A:LEU111 4.9 16.4 1.0
O A:HOH392 4.9 17.7 1.0
CG A:ARG97 4.9 17.0 1.0
CZ A:ARG97 5.0 23.2 1.0
HD2 A:ARG97 5.0 23.1 1.0

Iodine binding site 2 out of 4 in 6dog

Go back to Iodine Binding Sites List in 6dog
Iodine binding site 2 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:30.6
occ:0.40
O A:HOH453 3.2 37.6 1.0
HD3 A:LYS180 3.2 23.5 1.0
O A:HOH376 3.2 21.9 1.0
HG3 A:GLN134 3.2 31.0 1.0
HB2 A:LYS180 3.2 20.4 1.0
HA A:GLN134 3.3 18.8 1.0
O4 A:PGE216 3.6 35.0 1.0
HD12 A:ILE137 3.7 19.6 1.0
C6 A:PGE216 3.7 59.1 1.0
HG2 A:LYS180 3.9 22.4 1.0
O A:HOH456 3.9 51.2 1.0
CD A:LYS180 4.1 19.6 1.0
HG21 A:ILE137 4.1 18.4 1.0
CB A:LYS180 4.1 17.0 1.0
CG A:GLN134 4.1 25.9 1.0
HD13 A:ILE137 4.2 19.6 1.0
CA A:GLN134 4.2 15.7 1.0
CG A:LYS180 4.2 18.7 1.0
HB A:ILE137 4.2 17.1 1.0
HB2 A:GLN134 4.3 25.8 1.0
CD1 A:ILE137 4.4 16.4 1.0
HE21 A:GLN134 4.4 35.8 1.0
CB A:GLN134 4.4 21.5 1.0
HB3 A:LYS180 4.5 20.4 1.0
O A:HOH451 4.6 37.4 1.0
HE3 A:LYS180 4.6 25.7 1.0
HG2 A:GLN134 4.6 31.0 1.0
CE A:LYS180 4.8 21.4 1.0
HD2 A:LYS180 4.8 23.5 1.0
CG2 A:ILE137 4.8 15.3 1.0
HE2 A:LYS180 4.8 25.7 1.0
HG22 A:ILE137 4.9 18.4 1.0
CB A:ILE137 4.9 14.3 1.0
O A:GLN134 4.9 17.7 1.0

Iodine binding site 3 out of 4 in 6dog

Go back to Iodine Binding Sites List in 6dog
Iodine binding site 3 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:29.9
occ:0.30
O A:HOH458 2.9 34.3 1.0
HD13 A:ILE64 2.9 42.2 1.0
HG2 A:PRO177 3.0 19.2 1.0
HD11 A:LEU179 3.2 22.8 1.0
HG3 A:PRO128 3.2 19.9 1.0
HB3 A:PRO128 3.5 15.5 1.0
CD1 A:ILE64 3.6 35.1 1.0
HB2 A:PRO177 3.6 19.2 1.0
HD11 A:ILE64 3.6 42.2 1.0
HD12 A:ILE64 3.7 42.2 1.0
HD21 A:LEU179 3.8 22.2 1.0
CG A:PRO177 3.9 16.0 1.0
HB3 A:PRO177 4.0 19.2 1.0
CB A:PRO177 4.0 16.0 1.0
CG A:PRO128 4.1 16.6 1.0
CD1 A:LEU179 4.1 19.0 1.0
CB A:PRO128 4.2 12.9 1.0
HG21 A:ILE64 4.2 26.6 1.0
HG3 A:PRO177 4.3 19.2 1.0
HD13 A:LEU179 4.4 22.8 1.0
HD3 A:PRO128 4.4 14.6 1.0
HB2 A:PRO128 4.6 15.5 1.0
CD2 A:LEU179 4.6 18.5 1.0
HD12 A:LEU179 4.6 22.8 1.0
HG2 A:PRO128 4.7 19.9 1.0
HD2 A:PRO177 4.8 17.7 1.0
CG A:LEU179 4.8 16.1 1.0
CD A:PRO128 4.8 12.1 1.0
HD22 A:LEU179 4.9 22.2 1.0
HG A:LEU179 4.9 19.3 1.0
CG1 A:ILE64 4.9 30.3 1.0
CD A:PRO177 5.0 14.7 1.0
O A:HOH434 5.0 31.2 1.0

Iodine binding site 4 out of 4 in 6dog

Go back to Iodine Binding Sites List in 6dog
Iodine binding site 4 out of 4 in the Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Bacillus Halodurans Ribonuclease H1 in Complex with An Rna/Dna Hybrid: Reaction in 2 Mm MG2+ and 200 Mm K+ For 600 S at 21 C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I207

b:45.7
occ:0.35
HD2 A:HIS172 3.0 21.4 1.0
HE3 A:LYS121 3.5 28.4 1.0
HE2 A:LYS121 3.6 28.4 1.0
O A:HOH339 3.7 40.4 1.0
CD2 A:HIS172 3.8 17.9 1.0
O A:HOH440 3.8 46.8 1.0
CE A:LYS121 4.0 23.6 1.0
O A:HOH416 4.0 28.3 1.0
NE2 A:HIS172 4.2 21.1 1.0
O A:HOH408 4.4 29.6 1.0
HD3 A:LYS121 4.5 23.1 1.0
CD A:LYS121 4.9 19.2 1.0
HZ1 A:LYS121 5.0 26.6 1.0

Reference:

N.L.Samara, W.Yang. Cation Trafficking Propels Rna Hydrolysis. Nat. Struct. Mol. Biol. V. 25 715 2018.
ISSN: ESSN 1545-9985
PubMed: 30076410
DOI: 10.1038/S41594-018-0099-4
Page generated: Sun Aug 11 22:55:43 2024

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